Buggy code:
@ TestClass ( "org.openscience.cdk.formula.MolecularFormulaManipulatorTest" ) public class MolecularFormulaManipulator { @ TestMethod ( "testGetAtomCount_IMolecularFormula" ) public static int getAtomCount ( IMolecularFormula formula ) { } @ TestMethod ( "testGetElementCount_IMolecularFormula_IElement" ) public static int getElementCount ( IMolecularFormula formula , IElement element ) { } public static int getElementCount ( IMolecularFormula formula , IIsotope isotope ) { } public static int getElementCount ( IMolecularFormula formula , String symbol ) { } @ TestMethod ( "testGetIsotopes_IMolecularFormula_IElement" ) public static List < IIsotope > getIsotopes ( IMolecularFormula formula , IElement element ) { } @ TestMethod ( "testElements_IMolecularFormula" ) public static List < IElement > elements ( IMolecularFormula formula ) { } @ TestMethod ( "testContainsElement_IMolecularFormula_IElement" ) public static boolean containsElement ( IMolecularFormula formula , IElement element ) { } @ TestMethod ( "testRemoveElement_IMolecularFormula_IElement" ) public static IMolecularFormula removeElement ( IMolecularFormula formula , IElement element ) { } @ TestMethod ( "testGetString_IMolecularFormula_arrayString_boolean" ) public static String getString ( IMolecularFormula formula , String [ ] orderElements , boolean setOne ) { } @ TestMethod ( "testGetString_IMolecularFormula" ) public static String getString ( IMolecularFormula formula ) { } @ TestMethod ( "testGetString_IMolecularFormula_boolean" ) public static String getString ( IMolecularFormula formula , boolean setOne ) { } public static List < IIsotope > putInOrder ( String [ ] orderElements , IMolecularFormula formula ) { } @ TestMethod ( "testGetHillString_IMolecularFormula" ) @ Deprecated public static String getHillString ( IMolecularFormula formula ) { } @ TestMethod ( "testGetHTML_IMolecularFormula" ) public static String getHTML ( IMolecularFormula formula ) { } @ TestMethod ( "testGetHTML_IMolecularFormula_boolean_boolean" ) public static String getHTML ( IMolecularFormula formula , boolean chargeB , boolean isotopeB ) { } @ TestMethod ( "testGetHTML_IMolecularFormula_arrayString_boolean_boolean" ) public static String getHTML ( IMolecularFormula formula , String [ ] orderElements , boolean chargeB , boolean isotopeB ) { } @ TestMethod ( "testGetMolecularFormula_String_IChemObjectBuilder" ) public static IMolecularFormula getMolecularFormula ( String stringMF , IChemObjectBuilder builder ) { } @ TestMethod ( "testGetMajorIsotopeMolecularFormula_String_IChemObjectBuilder" ) public static IMolecularFormula getMajorIsotopeMolecularFormula ( String stringMF , IChemObjectBuilder builder ) { } private static IMolecularFormula getMolecularFormula ( String stringMF , boolean assumeMajorIsotope , IChemObjectBuilder builder ) { } @ TestMethod ( "testGetMolecularFormula_String_IMolecularFormula" ) public static IMolecularFormula getMolecularFormula ( String stringMF , IMolecularFormula formula ) { } private static IMolecularFormula getMolecularFormula ( String stringMF , IMolecularFormula formula , boolean assumeMajorIsotope ) { } private static String cleanMFfromCharge ( String formula ) { } private static int extractCharge ( String formula ) { } @ TestMethod ( "testGetTotalExactMass_IMolecularFormula" ) public static double getTotalExactMass ( IMolecularFormula formula ) { } private static double correctMass ( double mass , Integer charge ) { } @ TestMethod ( "testGetTotalMassNumber_IMolecularFormula" ) public static double getTotalMassNumber ( IMolecularFormula formula ) { } @ TestMethod ( "testGetNaturalExactMass_IMolecularFormula" ) public static double getNaturalExactMass ( IMolecularFormula formula ) { double mass = 0.0 ; IsotopeFactory factory ; try { factory = Isotopes . getInstance ( ) ; } catch ( IOException e ) { throw new RuntimeException ( "Could<seq2seq4repair_space>not<seq2seq4repair_space>instantiate<seq2seq4repair_space>the<seq2seq4repair_space>IsotopeFactory." ) ; } for ( IIsotope isotope : formula . isotopes ( ) ) { <START_BUG> IElement isotopesElement = isotope . getBuilder ( ) . newInstance ( IElement . class , isotope ) ; <END_BUG> mass += ( factory . getNaturalMass ( isotopesElement ) ) * ( formula . getIsotopeCount ( isotope ) ) ; } return mass ; } @ TestMethod ( "testGetMajorIsotopeMass_IMolecularFormula" ) public static double getMajorIsotopeMass ( IMolecularFormula formula ) { } @ TestMethod ( "testGetTotalNaturalAbundance_IMolecularFormula" ) public static double getTotalNaturalAbundance ( IMolecularFormula formula ) { } @ TestMethod ( "testGetDBE_IMolecularFormula" ) public static double getDBE ( IMolecularFormula formula ) throws CDKException { } @ TestMethod ( "testGetMolecularFormula_IAtomContainer" ) public static IMolecularFormula getMolecularFormula ( IAtomContainer atomContainer ) { } @ TestMethod ( "testGetMolecularFormula_IAtomContainer_IMolecularFormula" ) public static IMolecularFormula getMolecularFormula ( IAtomContainer atomContainer , IMolecularFormula formula ) { } @ TestMethod ( "testGetAtomContainer_IMolecularFormula" ) public static IAtomContainer getAtomContainer ( IMolecularFormula formula ) { } @ TestMethod ( "testGetAtomContainer_IMolecularFormula_IAtomContainer" ) public static IAtomContainer getAtomContainer ( IMolecularFormula formula , IAtomContainer atomContainer ) { } @ TestMethod ( "testGetAtomContainer_String_IChemObjectBuilder" ) public static IAtomContainer getAtomContainer ( String formulaString , IChemObjectBuilder builder ) { } public static String [ ] generateOrderEle ( ) { } private static String [ ] generateOrderEle_Hill_NoCarbons ( ) { } private static String [ ] generateOrderEle_Hill_WithCarbons ( ) { } @ TestMethod ( "testCompare_IMolecularFormula_IMolecularFormula" ) public static boolean compare ( IMolecularFormula formula1 , IMolecularFormula formula2 ) { } @ TestMethod ( "testGetHeavyElements_IMolecularFormula" ) public static List < IElement > getHeavyElements ( IMolecularFormula formula ) { } @ TestMethod ( "testSimplifyMolecularFormula_String" ) public static String simplifyMolecularFormula ( String formula ) { } private static String breakExtractor ( String formula ) { } private static String multipleExtractor ( String formula ) { } private static String muliplier ( String formula , int factor ) { } }

Fix:
IElement isotopesElement = formula . getBuilder ( ) . newInstance ( IElement . class , isotope ) ;